The main Naitō clan in Iwakidaira were transferred to Nobeoka Domain in distant Kyushu by the shogunate due to mismanagement in 1747; however, the Naitō of Yunagaya were blessed with a succession of able rulers (almost all of whom were adopted into the clan) and able retainers. The 4th daimyo, Naitō Masaatsu, codified the domain’s laws, and the 10th daimyo, Naitō Masatami established a domain academy. In 1855, significant coal deposits were found within the domain. At the time of the Meiji restoration, the 13th daimyo, Naitō Masayasu was still an infant. The domain joined the Ōuetsu Reppan Dōmei during the Boshin War, but was captured by Imperial forces without a struggle. The domain was reduced by only 1000 koku, and Masayasu was forced to abdicate in favor of the 14th and last daimyo, Naitō Masanori in 1869. He remained a domain governor until the abolition of the han system in July 1871.

As with most domains in the han system, Yunagaya Domain consisted of several discontinuous territories calculated to provide the assigned kokudaka, based on periodic cadastral surveys and projected agricultural yields.[1][2]